Starting phenix.real_space_refine on Sun Apr 14 21:40:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q97_13867/04_2024/7q97_13867.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q97_13867/04_2024/7q97_13867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q97_13867/04_2024/7q97_13867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q97_13867/04_2024/7q97_13867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q97_13867/04_2024/7q97_13867.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q97_13867/04_2024/7q97_13867.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 10622 2.51 5 N 3150 2.21 5 O 3258 1.98 5 H 15752 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32806 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 16403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1047, 16401 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 35, 'TRANS': 1011} Chain breaks: 9 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 1047, 16401 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 35, 'TRANS': 1011} Chain breaks: 9 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 16592 Chain: "B" Number of atoms: 16403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1047, 16401 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 35, 'TRANS': 1011} Chain breaks: 9 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 1047, 16401 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 35, 'TRANS': 1011} Chain breaks: 9 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 16592 Time building chain proxies: 28.09, per 1000 atoms: 0.86 Number of scatterers: 32806 At special positions: 0 Unit cell: (141.05, 128.31, 90.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 3258 8.00 N 3150 7.00 C 10622 6.00 H 15752 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.13 Conformation dependent library (CDL) restraints added in 6.3 seconds 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 16 sheets defined 4.2% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.620A pdb=" N THR A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 354 through 357 Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 1110 through 1115 removed outlier: 3.821A pdb=" N LYS A1113 " --> pdb=" O ASP A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1123 Processing helix chain 'A' and resid 1193 through 1195 No H-bonds generated for 'chain 'A' and resid 1193 through 1195' Processing helix chain 'A' and resid 1238 through 1242 Processing helix chain 'A' and resid 1327 through 1331 Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.620A pdb=" N THR B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 354 through 357 Processing helix chain 'B' and resid 706 through 708 No H-bonds generated for 'chain 'B' and resid 706 through 708' Processing helix chain 'B' and resid 1110 through 1115 removed outlier: 3.821A pdb=" N LYS B1113 " --> pdb=" O ASP B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1123 Processing helix chain 'B' and resid 1193 through 1195 No H-bonds generated for 'chain 'B' and resid 1193 through 1195' Processing helix chain 'B' and resid 1238 through 1242 Processing helix chain 'B' and resid 1327 through 1331 Processing sheet with id=AA1, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.493A pdb=" N PHE A 323 " --> pdb=" O TRP A 333 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 331 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 385 removed outlier: 6.093A pdb=" N LEU A 372 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 359 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 360 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 430 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 425 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N SER A 430 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 11.121A pdb=" N GLU A 423 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N LEU A 432 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N LEU A 421 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N LEU A 434 " --> pdb=" O TYR A 419 " (cutoff:3.500A) removed outlier: 13.272A pdb=" N TYR A 419 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 410 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 385 removed outlier: 6.093A pdb=" N LEU A 372 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 359 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 360 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 430 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 12.912A pdb=" N ARG A 433 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N TYR A 449 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER A 435 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS A 446 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU A 458 " --> pdb=" O HIS A 446 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU A 448 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 12.311A pdb=" N ARG A 454 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N TYR A 471 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TRP A 456 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 458 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 467 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN A 466 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA A 480 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 496 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 482 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA A 506 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 517 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP A 510 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 515 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 529 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE A 528 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG A 554 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR A 543 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL A 552 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N ARG A 551 " --> pdb=" O TYR A 567 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR A 567 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR A 553 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG A 585 " --> pdb=" O TYR A 597 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR A 597 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG A 587 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL A 595 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 617 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN A 610 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU A 615 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N GLN A 614 " --> pdb=" O TYR A 630 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N TYR A 630 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU A 616 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 627 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU A 639 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 629 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE A 637 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER A 648 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU A 661 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 650 " --> pdb=" O GLN A 659 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLN A 659 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 680 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 702 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL A 701 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS A 712 " --> pdb=" O HIS A 724 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N HIS A 724 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG A 714 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU A 722 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS A 743 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU A 764 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A 775 " --> pdb=" O THR A 788 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG A 806 " --> pdb=" O PHE A 818 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 828 " --> pdb=" O ASP A 819 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU A 827 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER A 848 " --> pdb=" O TYR A 860 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 857 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER A 873 " --> pdb=" O ALA A 857 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG A 859 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU A 871 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY A 861 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL A 869 " --> pdb=" O PHE A 897 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU A 906 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N THR A 926 " --> pdb=" O PHE A 942 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU A 951 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 961 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR A 971 " --> pdb=" O ARG A 983 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 993 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 992 " --> pdb=" O PHE A1004 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A1002 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP A1003 " --> pdb=" O THR A1016 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL A1013 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG A1033 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL A1063 " --> pdb=" O PHE A1078 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A1075 " --> pdb=" O ASP A1091 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP A1091 " --> pdb=" O ARG A1075 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A1077 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER A1089 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS A1079 " --> pdb=" O ILE A1087 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1126 through 1127 removed outlier: 3.874A pdb=" N GLU A1142 " --> pdb=" O ARG A1133 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE A1141 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL A1150 " --> pdb=" O GLN A1167 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN A1167 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A1163 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A1162 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A1187 " --> pdb=" O ARG A1178 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A1186 " --> pdb=" O ARG A1202 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG A1202 " --> pdb=" O ILE A1186 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A1188 " --> pdb=" O GLU A1200 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A1200 " --> pdb=" O LYS A1188 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU A1190 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A1211 " --> pdb=" O TYR A1222 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A1232 " --> pdb=" O TYR A1247 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A1257 " --> pdb=" O HIS A1248 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN A1256 " --> pdb=" O ALA A1269 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A1267 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN A1268 " --> pdb=" O ILE A1281 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE A1281 " --> pdb=" O GLN A1268 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG A1270 " --> pdb=" O GLU A1279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1313 through 1314 removed outlier: 3.549A pdb=" N ARG A1319 " --> pdb=" O ASP A1314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1344 through 1345 Processing sheet with id=AA9, first strand: chain 'B' and resid 300 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.493A pdb=" N PHE B 323 " --> pdb=" O TRP B 333 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 331 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AB3, first strand: chain 'B' and resid 381 through 385 removed outlier: 6.094A pdb=" N LEU B 372 " --> pdb=" O MET B 384 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 359 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 360 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER B 430 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 425 " --> pdb=" O ASP B 428 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N SER B 430 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 11.121A pdb=" N GLU B 423 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LEU B 432 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N LEU B 421 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 10.777A pdb=" N LEU B 434 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 13.272A pdb=" N TYR B 419 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 410 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 381 through 385 removed outlier: 6.094A pdb=" N LEU B 372 " --> pdb=" O MET B 384 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 359 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 360 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER B 430 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 12.912A pdb=" N ARG B 433 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N TYR B 449 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER B 435 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS B 446 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 458 " --> pdb=" O HIS B 446 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU B 448 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 12.311A pdb=" N ARG B 454 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N TYR B 471 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TRP B 456 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 458 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 467 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLN B 466 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA B 480 " --> pdb=" O SER B 496 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 496 " --> pdb=" O ALA B 480 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 482 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA B 506 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 517 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP B 510 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 515 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 529 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE B 528 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG B 554 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR B 543 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL B 552 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N ARG B 551 " --> pdb=" O TYR B 567 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR B 567 " --> pdb=" O ARG B 551 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR B 553 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG B 585 " --> pdb=" O TYR B 597 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR B 597 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG B 587 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL B 595 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 617 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN B 610 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU B 615 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 11.434A pdb=" N GLN B 614 " --> pdb=" O TYR B 630 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N TYR B 630 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B 616 " --> pdb=" O TYR B 628 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 627 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU B 639 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 629 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE B 637 " --> pdb=" O THR B 649 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N SER B 648 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU B 661 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 650 " --> pdb=" O GLN B 659 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLN B 659 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE B 680 " --> pdb=" O TYR B 692 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 702 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL B 701 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS B 712 " --> pdb=" O HIS B 724 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N HIS B 724 " --> pdb=" O LYS B 712 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG B 714 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU B 722 " --> pdb=" O PHE B 734 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS B 743 " --> pdb=" O PHE B 755 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU B 764 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 775 " --> pdb=" O THR B 788 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG B 806 " --> pdb=" O PHE B 818 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 828 " --> pdb=" O ASP B 819 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU B 827 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER B 848 " --> pdb=" O TYR B 860 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 857 " --> pdb=" O SER B 873 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER B 873 " --> pdb=" O ALA B 857 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG B 859 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 871 " --> pdb=" O ARG B 859 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY B 861 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL B 869 " --> pdb=" O PHE B 897 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU B 906 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N THR B 926 " --> pdb=" O PHE B 942 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU B 951 " --> pdb=" O HIS B 962 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 961 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR B 971 " --> pdb=" O ARG B 983 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 993 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 992 " --> pdb=" O PHE B1004 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B1002 " --> pdb=" O ILE B 994 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP B1003 " --> pdb=" O THR B1016 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL B1013 " --> pdb=" O SER B1024 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG B1033 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL B1063 " --> pdb=" O PHE B1078 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B1075 " --> pdb=" O ASP B1091 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP B1091 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU B1077 " --> pdb=" O SER B1089 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER B1089 " --> pdb=" O LEU B1077 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS B1079 " --> pdb=" O ILE B1087 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1126 through 1127 removed outlier: 3.875A pdb=" N GLU B1142 " --> pdb=" O ARG B1133 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE B1141 " --> pdb=" O PHE B1153 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B1150 " --> pdb=" O GLN B1167 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B1167 " --> pdb=" O VAL B1150 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B1163 " --> pdb=" O ALA B1154 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE B1162 " --> pdb=" O MET B1177 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B1187 " --> pdb=" O ARG B1178 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE B1186 " --> pdb=" O ARG B1202 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG B1202 " --> pdb=" O ILE B1186 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS B1188 " --> pdb=" O GLU B1200 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU B1200 " --> pdb=" O LYS B1188 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU B1190 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU B1211 " --> pdb=" O TYR B1222 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B1232 " --> pdb=" O TYR B1247 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN B1257 " --> pdb=" O HIS B1248 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN B1256 " --> pdb=" O ALA B1269 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B1267 " --> pdb=" O LEU B1258 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN B1268 " --> pdb=" O ILE B1281 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE B1281 " --> pdb=" O GLN B1268 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG B1270 " --> pdb=" O GLU B1279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1313 through 1314 removed outlier: 3.549A pdb=" N ARG B1319 " --> pdb=" O ASP B1314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1344 through 1345 558 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.66 Time building geometry restraints manager: 26.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15740 1.03 - 1.23: 25 1.23 - 1.42: 7875 1.42 - 1.62: 9516 1.62 - 1.81: 36 Bond restraints: 33192 Sorted by residual: bond pdb=" CG LEU A 826 " pdb=" CD1 LEU A 826 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CG LEU B 826 " pdb=" CD1 LEU B 826 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 bond pdb=" CG LEU B 505 " pdb=" CD1 LEU B 505 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.71e+00 bond pdb=" CG LEU A 505 " pdb=" CD1 LEU A 505 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 bond pdb=" CB ILE B1317 " pdb=" CG2 ILE B1317 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 ... (remaining 33187 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.18: 210 105.18 - 112.42: 34946 112.42 - 119.66: 9620 119.66 - 126.91: 14105 126.91 - 134.15: 255 Bond angle restraints: 59136 Sorted by residual: angle pdb=" N PRO B 731 " pdb=" CA PRO B 731 " pdb=" C PRO B 731 " ideal model delta sigma weight residual 111.68 114.97 -3.29 1.67e+00 3.59e-01 3.89e+00 angle pdb=" N PRO A 731 " pdb=" CA PRO A 731 " pdb=" C PRO A 731 " ideal model delta sigma weight residual 111.68 114.97 -3.29 1.67e+00 3.59e-01 3.87e+00 angle pdb=" CA LEU A 445 " pdb=" CB LEU A 445 " pdb=" CG LEU A 445 " ideal model delta sigma weight residual 116.30 122.80 -6.50 3.50e+00 8.16e-02 3.45e+00 angle pdb=" CA LEU B 445 " pdb=" CB LEU B 445 " pdb=" CG LEU B 445 " ideal model delta sigma weight residual 116.30 122.78 -6.48 3.50e+00 8.16e-02 3.43e+00 angle pdb=" N ALA B 638 " pdb=" CA ALA B 638 " pdb=" C ALA B 638 " ideal model delta sigma weight residual 109.06 112.16 -3.10 1.70e+00 3.46e-01 3.33e+00 ... (remaining 59131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 14899 17.86 - 35.73: 607 35.73 - 53.59: 159 53.59 - 71.46: 39 71.46 - 89.32: 10 Dihedral angle restraints: 15714 sinusoidal: 8446 harmonic: 7268 Sorted by residual: dihedral pdb=" CA TYR A 985 " pdb=" C TYR A 985 " pdb=" N TYR A 986 " pdb=" CA TYR A 986 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA TYR B 985 " pdb=" C TYR B 985 " pdb=" N TYR B 986 " pdb=" CA TYR B 986 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU B 991 " pdb=" C LEU B 991 " pdb=" N HIS B 992 " pdb=" CA HIS B 992 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 15711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1400 0.032 - 0.064: 614 0.064 - 0.095: 288 0.095 - 0.127: 99 0.127 - 0.159: 15 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CA PRO B 305 " pdb=" N PRO B 305 " pdb=" C PRO B 305 " pdb=" CB PRO B 305 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PRO A 305 " pdb=" N PRO A 305 " pdb=" C PRO A 305 " pdb=" CB PRO A 305 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL B 902 " pdb=" N VAL B 902 " pdb=" C VAL B 902 " pdb=" CB VAL B 902 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 2413 not shown) Planarity restraints: 5168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B1283 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO B1284 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B1284 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1284 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1283 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO A1284 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1284 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1284 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1035 " 0.107 9.50e-02 1.11e+02 3.59e-02 1.45e+00 pdb=" NE ARG A1035 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A1035 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A1035 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1035 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A1035 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A1035 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A1035 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A1035 " 0.001 2.00e-02 2.50e+03 ... (remaining 5165 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1182 2.15 - 2.76: 61107 2.76 - 3.38: 78518 3.38 - 3.99: 109224 3.99 - 4.60: 172516 Nonbonded interactions: 422547 Sorted by model distance: nonbonded pdb=" O ILE B 594 " pdb=" HE1 TRP B 609 " model vdw 1.539 1.850 nonbonded pdb=" O ILE A 594 " pdb=" HE1 TRP A 609 " model vdw 1.540 1.850 nonbonded pdb=" OD1 ASP B1007 " pdb=" H ARG B1011 " model vdw 1.549 1.850 nonbonded pdb=" OD1 ASP A1007 " pdb=" H ARG A1011 " model vdw 1.550 1.850 nonbonded pdb=" O LEU B 905 " pdb=" HH TYR B 919 " model vdw 1.553 1.850 ... (remaining 422542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 268 through 488 or resid 490 through 932 or resid 934 thro \ ugh 1461)) selection = (chain 'B' and (resid 268 through 488 or resid 490 through 932 or resid 934 thro \ ugh 1461)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.510 Extract box with map and model: 7.070 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 124.670 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 17440 Z= 0.588 Angle : 0.648 6.499 23610 Z= 0.334 Chirality : 0.045 0.159 2416 Planarity : 0.005 0.054 3164 Dihedral : 10.047 89.324 6448 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 0.56 % Allowed : 2.03 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 2054 helix: -0.24 (1.16), residues: 20 sheet: 1.47 (0.21), residues: 650 loop : -0.88 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 605 HIS 0.007 0.001 HIS B 555 PHE 0.010 0.002 PHE B 818 TYR 0.017 0.002 TYR A 837 ARG 0.006 0.001 ARG A1185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 377 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 367 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 SER cc_start: 0.7796 (p) cc_final: 0.7467 (p) REVERT: A 1027 ASP cc_start: 0.7032 (m-30) cc_final: 0.6800 (m-30) REVERT: A 1202 ARG cc_start: 0.6799 (ptp-170) cc_final: 0.6539 (mmm160) REVERT: B 428 ASP cc_start: 0.5831 (t0) cc_final: 0.5579 (t0) REVERT: B 451 SER cc_start: 0.8004 (p) cc_final: 0.7685 (p) REVERT: B 1009 LEU cc_start: 0.7021 (mp) cc_final: 0.6802 (mp) REVERT: B 1027 ASP cc_start: 0.6960 (m-30) cc_final: 0.6699 (m-30) outliers start: 10 outliers final: 2 residues processed: 377 average time/residue: 0.8268 time to fit residues: 433.1528 Evaluate side-chains 229 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 758 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1019 GLN A1218 GLN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 GLN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17440 Z= 0.161 Angle : 0.505 4.460 23610 Z= 0.266 Chirality : 0.040 0.153 2416 Planarity : 0.004 0.052 3164 Dihedral : 4.627 58.722 2396 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.12 % Favored : 96.79 % Rotamer: Outliers : 1.35 % Allowed : 6.14 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 2054 helix: 0.12 (1.27), residues: 20 sheet: 1.52 (0.19), residues: 734 loop : -0.86 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 669 HIS 0.007 0.001 HIS A 530 PHE 0.008 0.001 PHE B1412 TYR 0.012 0.001 TYR B 374 ARG 0.003 0.000 ARG B1282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ASP cc_start: 0.5979 (t0) cc_final: 0.5747 (m-30) REVERT: A 1027 ASP cc_start: 0.7214 (m-30) cc_final: 0.6893 (m-30) REVERT: B 439 ASP cc_start: 0.6028 (OUTLIER) cc_final: 0.5786 (m-30) REVERT: B 1027 ASP cc_start: 0.7200 (m-30) cc_final: 0.6887 (m-30) outliers start: 24 outliers final: 13 residues processed: 267 average time/residue: 0.8654 time to fit residues: 318.2036 Evaluate side-chains 223 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 810 ASP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 204 optimal weight: 0.2980 chunk 168 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 555 HIS ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 555 HIS ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17440 Z= 0.229 Angle : 0.521 4.917 23610 Z= 0.277 Chirality : 0.039 0.148 2416 Planarity : 0.004 0.052 3164 Dihedral : 4.391 20.242 2392 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 1.86 % Allowed : 6.93 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2054 helix: -0.10 (1.27), residues: 20 sheet: 1.38 (0.20), residues: 714 loop : -0.99 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 669 HIS 0.006 0.001 HIS B 530 PHE 0.007 0.001 PHE B1310 TYR 0.015 0.002 TYR A 374 ARG 0.004 0.000 ARG A 778 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 ASP cc_start: 0.7280 (m-30) cc_final: 0.7006 (m-30) REVERT: A 1459 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 762 ARG cc_start: 0.7862 (mtp180) cc_final: 0.7638 (mmp-170) REVERT: B 1027 ASP cc_start: 0.7226 (m-30) cc_final: 0.6946 (m-30) outliers start: 33 outliers final: 25 residues processed: 224 average time/residue: 0.8988 time to fit residues: 273.5260 Evaluate side-chains 216 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 1037 GLN Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 TRP Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 810 ASP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1103 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1214 GLN ** A1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17440 Z= 0.276 Angle : 0.557 5.624 23610 Z= 0.298 Chirality : 0.040 0.148 2416 Planarity : 0.004 0.052 3164 Dihedral : 4.708 19.779 2392 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.31 % Allowed : 6.98 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2054 helix: -0.57 (1.29), residues: 20 sheet: 1.22 (0.19), residues: 764 loop : -1.11 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 669 HIS 0.006 0.001 HIS B 530 PHE 0.011 0.002 PHE B1310 TYR 0.016 0.002 TYR B 374 ARG 0.005 0.001 ARG B 778 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 200 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 ASP cc_start: 0.7297 (m-30) cc_final: 0.7021 (m-30) REVERT: B 1027 ASP cc_start: 0.7237 (m-30) cc_final: 0.6964 (m-30) outliers start: 41 outliers final: 32 residues processed: 227 average time/residue: 0.7833 time to fit residues: 253.0329 Evaluate side-chains 223 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 932 ASP Chi-restraints excluded: chain A residue 1037 GLN Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 TRP Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 810 ASP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1206 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1249 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1249 ASN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17440 Z= 0.332 Angle : 0.579 5.864 23610 Z= 0.311 Chirality : 0.041 0.146 2416 Planarity : 0.004 0.053 3164 Dihedral : 4.896 21.949 2392 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 2.53 % Allowed : 7.88 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2054 helix: -1.44 (1.13), residues: 20 sheet: 1.02 (0.19), residues: 768 loop : -1.30 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.007 0.001 HIS A 530 PHE 0.013 0.002 PHE A1458 TYR 0.017 0.002 TYR A 374 ARG 0.005 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 ASP cc_start: 0.7312 (m-30) cc_final: 0.7043 (m-30) REVERT: B 997 ASP cc_start: 0.5939 (p0) cc_final: 0.5738 (p0) REVERT: B 1027 ASP cc_start: 0.7265 (m-30) cc_final: 0.6987 (m-30) outliers start: 45 outliers final: 37 residues processed: 222 average time/residue: 0.7796 time to fit residues: 245.1281 Evaluate side-chains 221 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 932 ASP Chi-restraints excluded: chain A residue 1037 GLN Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 TRP Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1206 ASP Chi-restraints excluded: chain B residue 1278 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 HIS B1214 GLN ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17440 Z= 0.239 Angle : 0.524 5.231 23610 Z= 0.282 Chirality : 0.039 0.142 2416 Planarity : 0.004 0.052 3164 Dihedral : 4.678 19.035 2392 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 2.03 % Allowed : 8.90 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2054 helix: -1.37 (1.12), residues: 20 sheet: 0.97 (0.19), residues: 768 loop : -1.33 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 669 HIS 0.006 0.001 HIS B 530 PHE 0.008 0.001 PHE A1412 TYR 0.014 0.002 TYR B 374 ARG 0.006 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 ASP cc_start: 0.7297 (m-30) cc_final: 0.7015 (m-30) REVERT: B 1027 ASP cc_start: 0.7265 (m-30) cc_final: 0.6983 (m-30) outliers start: 36 outliers final: 33 residues processed: 219 average time/residue: 0.7830 time to fit residues: 246.3176 Evaluate side-chains 215 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 932 ASP Chi-restraints excluded: chain A residue 1037 GLN Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 TRP Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 810 ASP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1206 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 17440 Z= 0.302 Angle : 0.560 5.624 23610 Z= 0.302 Chirality : 0.040 0.144 2416 Planarity : 0.004 0.053 3164 Dihedral : 4.808 20.443 2392 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.40 % Favored : 94.50 % Rotamer: Outliers : 2.42 % Allowed : 8.56 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2054 helix: -1.65 (1.08), residues: 20 sheet: 0.90 (0.19), residues: 778 loop : -1.42 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 669 HIS 0.007 0.001 HIS A 530 PHE 0.009 0.001 PHE B1310 TYR 0.016 0.002 TYR B 374 ARG 0.006 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 ASP cc_start: 0.7302 (m-30) cc_final: 0.7020 (m-30) REVERT: B 1027 ASP cc_start: 0.7279 (m-30) cc_final: 0.7008 (m-30) outliers start: 43 outliers final: 42 residues processed: 211 average time/residue: 0.7650 time to fit residues: 230.1771 Evaluate side-chains 223 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 932 ASP Chi-restraints excluded: chain A residue 1037 GLN Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 TRP Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 810 ASP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1206 ASP Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1214 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17440 Z= 0.226 Angle : 0.519 5.192 23610 Z= 0.279 Chirality : 0.039 0.139 2416 Planarity : 0.004 0.051 3164 Dihedral : 4.621 18.401 2392 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 2.31 % Allowed : 8.90 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2054 helix: -1.21 (1.14), residues: 20 sheet: 0.93 (0.19), residues: 780 loop : -1.37 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 669 HIS 0.006 0.001 HIS B 530 PHE 0.007 0.001 PHE A1458 TYR 0.014 0.001 TYR B 374 ARG 0.007 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 ASP cc_start: 0.7308 (m-30) cc_final: 0.7010 (m-30) REVERT: B 1027 ASP cc_start: 0.7260 (m-30) cc_final: 0.6981 (m-30) outliers start: 41 outliers final: 39 residues processed: 207 average time/residue: 0.7883 time to fit residues: 231.7856 Evaluate side-chains 215 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 932 ASP Chi-restraints excluded: chain A residue 1037 GLN Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 TRP Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 810 ASP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1206 ASP Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1214 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17440 Z= 0.246 Angle : 0.530 5.330 23610 Z= 0.285 Chirality : 0.039 0.140 2416 Planarity : 0.004 0.051 3164 Dihedral : 4.634 18.400 2392 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.45 % Rotamer: Outliers : 2.42 % Allowed : 8.90 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2054 helix: -1.32 (1.10), residues: 20 sheet: 0.89 (0.19), residues: 784 loop : -1.39 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 669 HIS 0.007 0.001 HIS A 530 PHE 0.007 0.001 PHE B1310 TYR 0.014 0.002 TYR A 374 ARG 0.007 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 ASP cc_start: 0.7311 (m-30) cc_final: 0.7014 (m-30) REVERT: B 1027 ASP cc_start: 0.7257 (m-30) cc_final: 0.6985 (m-30) outliers start: 43 outliers final: 41 residues processed: 212 average time/residue: 0.7699 time to fit residues: 232.2352 Evaluate side-chains 222 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 932 ASP Chi-restraints excluded: chain A residue 1037 GLN Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 TRP Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 810 ASP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1206 ASP Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1214 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 93 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 165 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17440 Z= 0.116 Angle : 0.470 4.897 23610 Z= 0.252 Chirality : 0.038 0.132 2416 Planarity : 0.003 0.049 3164 Dihedral : 4.258 17.422 2392 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 1.41 % Allowed : 9.80 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 2054 helix: -0.47 (1.26), residues: 20 sheet: 1.15 (0.19), residues: 758 loop : -1.27 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 669 HIS 0.006 0.001 HIS A 530 PHE 0.006 0.001 PHE A1307 TYR 0.010 0.001 TYR A1286 ARG 0.007 0.000 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ARG cc_start: 0.7678 (ttm170) cc_final: 0.6919 (mtp180) REVERT: A 1027 ASP cc_start: 0.7277 (m-30) cc_final: 0.6974 (m-30) REVERT: B 1027 ASP cc_start: 0.7238 (m-30) cc_final: 0.6917 (m-30) outliers start: 25 outliers final: 24 residues processed: 212 average time/residue: 0.7933 time to fit residues: 240.4786 Evaluate side-chains 211 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 810 ASP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.158423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139574 restraints weight = 55217.069| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.74 r_work: 0.3483 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17440 Z= 0.191 Angle : 0.494 4.982 23610 Z= 0.265 Chirality : 0.039 0.138 2416 Planarity : 0.003 0.049 3164 Dihedral : 4.302 17.665 2392 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.38 % Favored : 95.52 % Rotamer: Outliers : 1.58 % Allowed : 9.91 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2054 helix: -0.58 (1.22), residues: 20 sheet: 1.16 (0.19), residues: 772 loop : -1.28 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 669 HIS 0.005 0.001 HIS A 530 PHE 0.007 0.001 PHE A1458 TYR 0.012 0.001 TYR A 374 ARG 0.008 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7161.34 seconds wall clock time: 128 minutes 16.05 seconds (7696.05 seconds total)